[2024-01-25 19:53:20,655] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:53:20,656] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:53:20,656] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f1129ab-9fbc-4766-aa4b-002ba6b7e9ee/dqc_reference
[2024-01-25 19:53:21,794] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:53:21,794] [INFO] Task started: Prodigal
[2024-01-25 19:53:21,794] [INFO] Running command: gunzip -c /var/lib/cwl/stgf208b938-3ca1-4ff1-91d8-eec9b94e9e2d/GCF_000438455.1_Nosocomiicoccus_NP2_v1_genomic.fna.gz | prodigal -d GCF_000438455.1_Nosocomiicoccus_NP2_v1_genomic.fna/cds.fna -a GCF_000438455.1_Nosocomiicoccus_NP2_v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:53:24,041] [INFO] Task succeeded: Prodigal
[2024-01-25 19:53:24,042] [INFO] Task started: HMMsearch
[2024-01-25 19:53:24,042] [INFO] Running command: hmmsearch --tblout GCF_000438455.1_Nosocomiicoccus_NP2_v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f1129ab-9fbc-4766-aa4b-002ba6b7e9ee/dqc_reference/reference_markers.hmm GCF_000438455.1_Nosocomiicoccus_NP2_v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:53:24,246] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:53:24,247] [INFO] Found 6/6 markers.
[2024-01-25 19:53:24,263] [INFO] Query marker FASTA was written to GCF_000438455.1_Nosocomiicoccus_NP2_v1_genomic.fna/markers.fasta
[2024-01-25 19:53:24,263] [INFO] Task started: Blastn
[2024-01-25 19:53:24,263] [INFO] Running command: blastn -query GCF_000438455.1_Nosocomiicoccus_NP2_v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f1129ab-9fbc-4766-aa4b-002ba6b7e9ee/dqc_reference/reference_markers.fasta -out GCF_000438455.1_Nosocomiicoccus_NP2_v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:24,820] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:24,823] [INFO] Selected 18 target genomes.
[2024-01-25 19:53:24,823] [INFO] Target genome list was writen to GCF_000438455.1_Nosocomiicoccus_NP2_v1_genomic.fna/target_genomes.txt
[2024-01-25 19:53:24,863] [INFO] Task started: fastANI
[2024-01-25 19:53:24,863] [INFO] Running command: fastANI --query /var/lib/cwl/stgf208b938-3ca1-4ff1-91d8-eec9b94e9e2d/GCF_000438455.1_Nosocomiicoccus_NP2_v1_genomic.fna.gz --refList GCF_000438455.1_Nosocomiicoccus_NP2_v1_genomic.fna/target_genomes.txt --output GCF_000438455.1_Nosocomiicoccus_NP2_v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:53:31,482] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:31,483] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f1129ab-9fbc-4766-aa4b-002ba6b7e9ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:53:31,483] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f1129ab-9fbc-4766-aa4b-002ba6b7e9ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:53:31,488] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:53:31,488] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:53:31,488] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Nosocomiicoccus massiliensis	strain=NP2	GCA_000438455.1	1232430	1232430	type	True	100.0	419	425	95	conclusive
Nosocomiicoccus ampullae	strain=DSM 19163	GCA_019357495.1	489910	489910	type	True	82.1146	316	425	95	below_threshold
Nosocomiicoccus ampullae	strain=DSM 19163	GCA_014202595.1	489910	489910	type	True	82.109	312	425	95	below_threshold
Aliicoccus persicus	strain=IBRC-M10081	GCA_900110815.1	930138	930138	type	True	76.9912	52	425	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:53:31,489] [INFO] DFAST Taxonomy check result was written to GCF_000438455.1_Nosocomiicoccus_NP2_v1_genomic.fna/tc_result.tsv
[2024-01-25 19:53:31,490] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:53:31,490] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:53:31,490] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f1129ab-9fbc-4766-aa4b-002ba6b7e9ee/dqc_reference/checkm_data
[2024-01-25 19:53:31,491] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:53:31,508] [INFO] Task started: CheckM
[2024-01-25 19:53:31,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000438455.1_Nosocomiicoccus_NP2_v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000438455.1_Nosocomiicoccus_NP2_v1_genomic.fna/checkm_input GCF_000438455.1_Nosocomiicoccus_NP2_v1_genomic.fna/checkm_result
[2024-01-25 19:53:44,861] [INFO] Task succeeded: CheckM
[2024-01-25 19:53:44,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:53:44,883] [INFO] ===== Completeness check finished =====
[2024-01-25 19:53:44,883] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:53:44,883] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000438455.1_Nosocomiicoccus_NP2_v1_genomic.fna/markers.fasta)
[2024-01-25 19:53:44,884] [INFO] Task started: Blastn
[2024-01-25 19:53:44,884] [INFO] Running command: blastn -query GCF_000438455.1_Nosocomiicoccus_NP2_v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f1129ab-9fbc-4766-aa4b-002ba6b7e9ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_000438455.1_Nosocomiicoccus_NP2_v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:45,627] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:45,630] [INFO] Selected 12 target genomes.
[2024-01-25 19:53:45,630] [INFO] Target genome list was writen to GCF_000438455.1_Nosocomiicoccus_NP2_v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:53:45,639] [INFO] Task started: fastANI
[2024-01-25 19:53:45,639] [INFO] Running command: fastANI --query /var/lib/cwl/stgf208b938-3ca1-4ff1-91d8-eec9b94e9e2d/GCF_000438455.1_Nosocomiicoccus_NP2_v1_genomic.fna.gz --refList GCF_000438455.1_Nosocomiicoccus_NP2_v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000438455.1_Nosocomiicoccus_NP2_v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:53:49,768] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:49,773] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:53:49,773] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000438455.1	s__Nosocomiicoccus massiliensis	100.0	419	425	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Nosocomiicoccus	95.642	100.00	100.00	0.99	0.99	2	conclusive
GCF_001696685.1	s__Nosocomiicoccus ampullae_A	95.642	384	425	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Nosocomiicoccus	95.642	98.29	98.16	0.91	0.90	5	conclusive
GCF_014202595.1	s__Nosocomiicoccus ampullae	82.109	312	425	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Nosocomiicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119225.1	s__Nosocomiicoccus stercorigallinarum	82.0573	277	425	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Nosocomiicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110815.1	s__Aliicoccus persicus	76.946	53	425	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Aliicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:53:49,774] [INFO] GTDB search result was written to GCF_000438455.1_Nosocomiicoccus_NP2_v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:53:49,775] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:53:49,777] [INFO] DFAST_QC result json was written to GCF_000438455.1_Nosocomiicoccus_NP2_v1_genomic.fna/dqc_result.json
[2024-01-25 19:53:49,777] [INFO] DFAST_QC completed!
[2024-01-25 19:53:49,777] [INFO] Total running time: 0h0m29s